Dear Amber community,
I have been trying to use MMPBSA module in AmberTools12 package for binding
affinity calculations during the past weeks on TACC clusters.
However, I constantly receive the following error as soon as calculations
reach the PBSA part:
CalcError: /opt/apps/intel11_1/mvapich2_1_6/amber/12.0/bin/mmpbsa_py_energy
failed with prmtop
/work/01902/ashahmor/mmpbsa/setup/1JIW_PI/antemmpbsa/1JIW_PI.prmtop!
PB bomb in pb_setgrd(): Allocation aborted 0
0 0
Similarly, when I turn on the entropy option (entropy=1), or use
mmpbsa_py_nabnmode for entropy calculations, I get the following error:
CalcError:
/opt/apps/intel11_1/mvapich2_1_6/amber/12.0/bin/mmpbsa_py_nabnmode failed
with prmtop
/work/01902/ashahmor/mmpbsa/setup/1B6C_AB/antemmpbsa/1B6C_AB.prmtop!
I have already read almost all relevant posts in Amber mailing list about
similar errors, and I have tried every single suggested solution. But, none
of them work to this date.
It seems that there is some inconsistency between the topology files
generated by tleap and the topology files that MMPBSA and ptraj modules
expect to have as input. In contrast to PBSA, GBSA runs with no problems or
errors for any of the structures that I have tried.
I use the following commands to generate the topology files for MD
simulations and modify them later by ante-mmpbsa to generate the topology
files for MMPBSA calculations:
> tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff12SB
> source leaprc.ff12SB
> loadamberparams frcmod.ionsjc_tip3p
Any help or suggestion to resolve these errors is highly appreciated.
Thank you,
Amir
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Received on Tue May 06 2014 - 17:30:02 PDT
